5ttgen fsl vs. 5ttgen freesurfer

Hello everyone,

I have a question regarding 5ttgen command. I’m trying to apply segmentation on the LEMON dataset that uses MP2RAGE sequence for T1 scans. I used this MATLAB-based tool to remove the background of the T1 scans: GitHub - JosePMarques/MP2RAGE-related-scripts: MP2RAGE Scripts - T1 map correction & Background no

Then I applied 5ttgen fsl and get the following results for GM:

However, 5ttgen freesurfer gives the following results which is slightly different:

Could you help me figure out which one is the preferred one?

Thank you very much for your time and help.

Best Regards,

Welcome Mahta!

I’ve not myself experimented with 5ttgen on MP2RAGE data, so there may yet be some nuances that I’ve not yet come across.

5ttgen freesurfer isn’t very commonly used: while it is based on FreeSurfer segmentation, which is appealing, it’s a simple voxel-by-voxel mapping of binary tissue masks, so there are no partial volume estimates, that’s why it appears so jagged. Indeed it was intended primarily as an exercise in demonstrating that multiple algorithms can be proposed and implemented and distributed for a given image processing task…

Version 3.0.0 comes with 5ttgen hsvs, which is described here and is my preferred solution.


1 Like

Hello Rob,

Thank you so much for your response. This is very helpful, I appreciate it.

Best Regards,